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Wednesday, January 29, 2014

A
reconstruction of a Neanderthal skeleton, right, with a modern human skeleton
in the background. Frank Franklin II/Associated Press.

The Little Bit of Neanderthal in All of Us. By Carl Zimmer. New York Times, January 29, 2014.Toe Fossil Provides Complete Neanderthal Genome. By Carl Zimmer. NJBR, December 20, 2013. With related articles.The genomic landscape of Neanderthal ancestry in present-day humans. By Siriram Sankararaman et al. Nature, published online January 29, 2014.Abstract:Genomic
studies have shown that Neanderthals interbred with modern humans, and that
non-Africans today are the products of this mixture. The antiquity of Neanderthal
gene flow into modern humans means that genomic regions that derive from
Neanderthals in any one human today are usually less than a hundred kilobases
in size. However, Neanderthal haplotypes are also distinctive enough that
several studies have been able to detect Neanderthal ancestry at specific loci.
We systematically infer Neanderthal haplotypes in the genomes of 1,004
present-day humans. Regions that harbour a high frequency of Neanderthal
alleles are enriched for genes affecting keratin filaments, suggesting that
Neanderthal alleles may have helped modern humans to adapt to non-African
environments. We identify multiple Neanderthal-derived alleles that confer risk
for disease, suggesting that Neanderthal alleles continue to shape human
biology. An unexpected finding is that regions with reduced Neanderthal
ancestry are enriched in genes, implying selection to remove genetic material
derived from Neanderthals. Genes that are more highly expressed in testes than
in any other tissue are especially reduced in Neanderthal ancestry, and there
is an approximately fivefold reduction of Neanderthal ancestry on the X
chromosome, which is known from studies of diverse species to be especially
dense in male hybrid sterility genes. These results suggest that part of the
explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal
alleles that caused decreased fertility in males when moved to a modern human
genetic background.The Date of Interbreeding between Neandertals and Modern Humans. By Siriram Sankararaman et al. PLOS Genetics, October 4, 2012. Also here.Abstract:Comparisons
of DNA sequences between Neandertals and present-day humans have shown that
Neandertals share more genetic variants with non-Africans than with Africans.
This could be due to interbreeding between Neandertals and modern humans when
the two groups met subsequent to the emergence of modern humans outside Africa.
However, it could also be due to population structure that antedates the origin
of Neandertal ancestors in Africa. We measure the extent of linkage
disequilibrium (LD) in the genomes of present-day Europeans and find that the
last gene flow from Neandertals (or their relatives) into Europeans likely
occurred 37,000–86,000 years before the present (BP), and most likely
47,000–65,000 years ago. This supports the recent interbreeding hypothesis and
suggests that interbreeding may have occurred when modern humans carrying Upper
Paleolithic technologies encountered Neandertals as they expanded out of
Africa.Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. By Benjamin Vernot and Joshua M. Akey. Science, published online January 29, 2014.Abstract:Anatomically
modern humans overlapped and mated with Neandertals such that non-African
humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified
Neandertal lineages that persist in the DNA of modern humans, in whole-genome
sequences from 379 European and 286 East Asian individuals, recovering over 15
Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR =
5%). Analyses of surviving archaic lineages suggests that there were fitness
costs to hybridization, admixture occurred both before and subsequent to
divergence of non-African modern humans, and Neandertals were a source of
adaptive variation for loci involved in skin phenotypes. Our results provide a
new avenue for paleogenomics studies, allowing substantial amounts of
population-level DNA sequence information to be obtained from extinct groups
even in the absence of fossilized remains.Zimmer:Ever
since the discovery in 2010 that Neanderthals interbred with the ancestors of
living humans, scientists have been trying to determine how their DNA affects
people today. Now two new studies have traced the history of Neanderthal DNA,
and have pinpointed a number of genes that may have medical importance today.

Among
the findings, the studies have found clues to the evolution of skin and
fertility, as well as susceptibility to diseases like diabetes. More broadly,
they show how the legacy of Neanderthals has endured 30,000 years after their
extinction.

“It’s
something that everyone wanted to know,” said Laurent Excoffier, a geneticist
at the University of Bern in Switzerland who was not involved in the research.

Neanderthals,
who became extinct about 30,000 years ago, were among the closest relatives of
modern humans. They shared a common ancestor with us that lived about 600,000
years ago.

In the
1990s, researchers began finding fragments of Neanderthal DNA in fossils. By
2010 they had reconstructed most of the Neanderthal genome. When they compared
it with the genomes of five living humans, they found similarities to small
portions of the DNA in the Europeans and Asians.

The
researchers concluded that Neanderthals and modern humans must have interbred.
Modern humans evolved in Africa and then expanded out into Asia and Europe,
where Neanderthals lived. In a 2012 study, the researchers estimated that this
interbreeding took place between 37,000 and 85,000 years ago.

Sir
Paul A. Mellars, an archaeologist at the University of Cambridge and the
University of Edinburgh, who was not involved in the research, said the
archaeological evidence suggested the opportunity for modern humans to mate
with Neanderthals would have been common once they expanded out of Africa.
“They’d be bumping into Neanderthals at every street corner,” he joked.

The
first draft of the Neanderthal genome was too rough to allow scientists to draw
further conclusions. But recently, researchers sequenced a far more accurate genome from a Neanderthal toe bone.

Scientists
at Harvard Medical School and the Max Planck Institute for Evolutionary
Anthropology in Germany compared this high-quality Neanderthal genome to the
genomes of 1,004 living people. They were able to identify specific segments of
Neanderthal DNA from each person’s genome.

“It’s a
personal map of Neanderthal ancestry,” said David Reich of Harvard Medical
School, who led the research team. He and his colleagues published their
results in the journal Nature.

Living
humans do not have a lot of Neanderthal DNA, Dr. Reich and his colleagues
found, but some Neanderthal genes have become very common. That’s because, with
natural selection, useful genes survive as species evolve. “What this proves is
that these genes were helpful for non-Africans in adapting to the environment,”
Dr. Reich said.

In a
separate study published in Science, Benjamin Vernot and Joshua M. Akey of the
University of Washington came to a similar conclusion, using a different
method.

Mr.
Vernot and Dr. Akey looked for unusual mutations in the genomes of 379
Europeans and 286 Asians. The segments of DNA that contained these mutations
turned out to be from Neanderthals.

Both
studies suggest that Neanderthal genes involved in skin and hair were favored
by natural selection in humans. Today, they are very common in living
non-Africans.

The
fact that two independent studies pinpointed these genes lends support to their
importance, said Sriram Sankararaman of Harvard Medical School, a co-author on
the Nature paper. “The two methods seem to be converging on the same results.”

It is
possible, Dr. Akey speculated, that the genes developed to help Neanderthal
skin adapt to the cold climate of Europe and Asia.

But Dr.
Akey pointed out that skin performs other important jobs, like shielding us
from pathogens. “We don’t understand enough about the biology of those
particular genes yet,” he said. “It makes it hard to pinpoint a reason why
they’re beneficial.”

Both
teams of scientists also found long stretches of the living human genomes where
Neanderthal DNA was glaringly absent. This pattern could be produced if modern
humans with certain Neanderthal genes could not have as many children on
average as people without them. For example, living humans have very few genes
from Neanderthals involved in making sperm. That suggests that male
human-Neanderthal hybrids might have had lower fertility or were even sterile.

Overall,
said Dr. Reich, “most of the Neanderthal genetic material was more bad than
good.”

Some of
the Neanderthal genes that have endured until today may be influencing people’s
health. Dr. Reich and his colleagues identified nine Neanderthal genes in
living humans that are known to raise or reduce the risk of various diseases,
including diabetes and lupus.

To
better understand the legacy of Neanderthals, Dr. Reich and his colleagues are
collaborating with the UK Biobank, which collects genetic information from
hundreds of thousands of volunteers. The scientists will search for Neanderthal
genetic markers, and investigate whether Neanderthal genes cause any noticeable
differences in anything from weight to blood pressure to scores on memory
tests.

“This
experiment of nature has been done,” said Dr. Reich, “and we can study it.”

One
infant’s skeleton found at the Hambleden site. An analysis of remains from 35
infants revealed they were most likely killed at birth. English Heritage.

Ancient Roman Infanticide Didn’t Spare Either Sex. By Stephanie Pappas. LiveScience, January 24, 2014. Also at Discovery News.Ancient DNA study of the remains of putative infanticide victims from the Yewden Roman villa site at Hambleden, England. By Naglaa Abu-Mandil Hassana, Keri A.
Brown, Jill Eyers, Terence A. Brown, and Simon Mays. Journal of Archaeological Science, Vol. 43 (March 2014).Abstract:Previous
analysis of the perinatal infant burials from Romano-British Yewden villa,
Hambleden, indicated the practice of infanticide at that site. We attempted to
determine whether this practice was specifically targeted at one sex or other
by determining the sex of the infants using analysis of fragments of the
amelogenin gene. We also analysed mtDNA in order to shed light on aspects of
kinship. Thirty-three infants were analysed, and sex was successfully identified
in 12. Seven were female, five male. No two infants shared identical mtDNA
polymorphisms, indicating that all came from different mothers. Taken together
with previous DNA results from perinatal remains from Romano-British sites
where infanticide has been identified, they provide no evidence that
manipulation of the sex ratio was a motivation for infanticide in Roman
Britain.

Pappas:A new
look at a cache of baby bones discovered in Britain is altering assumptions
about why ancient Romans committed infanticide.

Infant
girls were apparently not killed more often than baby boys, researchers report
in an upcoming issue of the Journal of
Archaeological Science.

“Very
often, societies have preferred male offspring, so when they practice
infanticide, it tends to be the male babies that are kept, and the female
babies that are killed,” said study researcher Simon Mays, a skeletal biologist
for English Heritage, a non-governmental organization that protects historic
sites.

Though
ancient Romans indeed preferred boys, there is no evidence they went as far as
infanticide to skew the sex ratio, Mays told LiveScience.

Tiny skeletons

Mays
and his colleagues used a technique called ancient DNA analysis to study infant
bones found at a site called Yewden Villa, near Hambleden, in England. Although
the site was first excavated in 1912, and found to hold the remains of infants
dating back about 1,800 years, the infant bones were since thought to have been
lost, Mays said.

But
recently, nearly a century after the initial excavation, archaeologist Jill
Eyers, director of Chiltern Archaeology in England, found the bones tucked away
in tiny boxes in the site archive.

In
2011, Mays and Eyers published a study of the bones suggesting the babies were
victims of infanticide, based on the fact that measurements of the long bones
of the arms and legs suggested that all of the babies died at the same age,
right at the time of birth.

If the
deaths had been natural, Mays said, you’d expect to see some premature babies,
some who died around the time of birth, and others who died in the weeks after
birth.

Because
of the high number of skeletons, the researchers speculated the site contained
a brothel, and the babies were those of prostitutes. But that idea was always “a
long shot,” Mays said.

In the
new study, the researchers delved into why these babies were killed. Ancient
Roman texts refer to infanticide as an accepted practice, and the only way people
could control the size of their families in a time before reliable
contraception. (In fact, Rome’s foundation myth involves twin boys, Romulus and
Remus, who are left to die by their mother, but are saved by wild animals.)

The
texts refer to infanticide in Rome itself, however, which had a different
culture than its far-flung territories, such as those in Britain, Mays said.

And
although the Roman preference for boys would suggest that Romans practiced
sex-selective infanticide, Mays said, there is only one document to back up
that assumption — a letter from one Roman soldier stationed in England to his
pregnant wife, telling her not to bother keeping the baby if it’s a girl when
it's born.

DNA testing

It’s impossible
to tell the sex of a baby by looking at the shape of the bones. Sex differences
only emerge after puberty, Mays said. So the researchers turned to a newer
tool: ancient DNA analysis. They tested 33 of the 35 most complete remains, but
because DNA does not preserve well in old bones, the researchers were able to
tease out sequences for only 12 of the 33.

Of
those, seven were female and five were male, a relatively even sex ratio, Mays
said.

What’s
more, none of the babies shared a mother, a strike against the brothel
hypothesis. If the babies were the offspring of prostitutes, Mays said, the
women would likely have been pregnant again and again.

The 12
babies studied in the new paper bring the total number of ancient Roman babies
thought to be victims of infanticide who have undergone DNA testing to 25.
Overall, there is no evidence that baby girls were killed more often.

“It
seems as though they weren’t using infanticide to manipulate the sex ratio,”
Mays said.

“Now
that we can use DNA to tell whether the babies were male or female, we’re
starting to revise the commonly held assumptions about infanticide in the Roman
world,” said Kristina Killgrove, a bioarchaeologist at the University of West
Florida, who was not involved in the research.

As
horrifying as the killing of newborns seems to modern people, in ancient Rome,
babies weren’t considered fully human upon birth, Mays said. Instead, they
gained humanity over time, first with their naming a few days after birth, and
later when they cut teeth and could eat solid food.

Growth and globalisation cannot cure all the world’s ills. By Gideon Rachman. The Financial Times, January 27, 2014.Rachman:In
Europe and North America it is the threat of political and social tensions
within nations, rather than international rivalries, that are worrying the
global plutocracy. A central element of the Davos creed is the faith that
globalisation is good for both the western world and for emerging powers.

However,
it is now almost conventional wisdom that the globalisation medicine has had an
unpleasant side-effect. Even if it raises overall growth levels it has also
powerfully contributed to wage stagnation and increasing inequality in the
west. As a result, European politicians are worrying about a possible
resurgence of the nationalist right and the radical left. And the Americans are
increasingly worried about the gap between the richest 1 per cent and the rest
– and the political consequences should the gulf keep widening.

It is
easy to mock the global plutocracy – fretting about war and inequality – as
they sip fine wines, behind a security perimeter high in the Swiss mountains.
Yet global bankers and business people are, at least, largely immune to the
viruses of xenophobia and nationalism. Their unofficial slogan is “make money,
not war”. And they treat foreigners as potential customers rather than
potential enemies.

In that
sense, the idea that capitalism and globalisation are the best antidotes to
political conflict – for all its flaws – retains a lot of attraction. Even if
the old economic treatments for political conflict are losing some of their
potency, they are still the best we have.